Browsing by Author "Assis, Jorge"
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- Bio‐ORACLE v3.0. pushing marine data layers to the CMIP6 earth system models of climate change researchPublication . Assis, Jorge; Fernández Bejarano, Salvador Jesús; Salazar, Vinícius W.; Schepers, Lennert; Gouvêa, Lidiane; Fragkopoulou, Eliza; Leclercq, Frederic; Vanhoorne, Bart; Tyberghein, Lennert; Serrao, Ester; Verbruggen, Heroen; De Clerck, OlivierMotivation: Impacts of climate change on marine biodiversity are often projected with species distribution modelling using standardized data layers representing physical, chemical and biological conditions of the global ocean. Yet, the available data layers (1) have not been updated to incorporate data of the Sixth Phase of the Coupled Model Intercomparison Project (CMIP6), which comprise the Shared Socioeconomic Pathway (SSP) scenarios; (2) consider a limited number of Earth System Models (ESMs), and (3) miss important variables expected to influence future biodiversity distributions. These limitations might undermine biodiversity impact assessments, by failing to integrate them within the context of the most up-to-date climate change projections, raising the uncertainty in estimates and misinterpreting the exposure of biodiversity to extreme conditions. Here, we provide a significant update of Bio-ORACLE, extending biologically relevant data layers from present-day conditions to the end of the 21st century Shared Socioeconomic Pathway scenarios based on a multi-model ensemble with data from CMIP6. Alongside, we provide R and Python packages for seamless integration in modelling workflows. The data layers aim to enhance the understanding of the potential impacts of climate change on biodiversity and to support well-informed research, conservation and management. Main Types of Variable Contained: Surface and benthic layers for, chlorophyll-a, diffuse attenuation coefficient, dissolved iron, dissolved oxygen, nitrate, ocean temperature, pH, phosphate, photosynthetic active radiation, total phytoplankton, total cloud fraction, salinity, silicate, sea-water direction, sea-water velocity, topographic slope, topographic aspect, terrain ruggedness index, topographic position index and bathymetry, and surface layers for air temperature, mixed layer depth, sea-ice cover and sea-ice thickness. Spatial Location and Grain: Global at 0.05 degrees resolution. Time Period and GrainDecadal from present-day to the end of the 21st century (2000-2100). Major Taxa and Level of Measurement: Marine biodiversity associated with surface and epibenthic habitats. Software Format: A package of functions developed for Python and R software.
- Biologically meaningful distribution models highlight the benefits of the Paris Agreement for demersal fishing targets in the North Atlantic OceanPublication . Ramos Martins, Manuel; Assis, Jorge; Abecasis, DavidAim: With climate change challenging marine biodiversity and resource management, it is crucial to anticipate future latitudinal and depth shifts under contrasting global change scenarios to support policy-relevant biodiversity impact assessments [e.g., Intergovernmental Panel on Climate Change (IPCC)]. We aim to demonstrate the benefits of complying with the Paris Agreement (United Nations Framework Convention on Climate Change) and limiting environmental changes, by assessing future distributional shifts of 10 commercially important demersal fish species. Location: Northern Atlantic Ocean. Time period: Analyses of distributional shifts compared near present-day conditions (2000–2017) with two Representative Concentration Pathway (RCP) scenarios of future climate changes (2090–2100): one following the Paris Agreement climate forcing (RCP2.6) and another without stringent mitigation measures (RCP8.5). Major taxa studied: Demersal fish. Methods: We use machine learning distribution models coupled with biologically meaningful predictors to project future latitudinal and depth shifts. Structuring projections with information beyond temperature-based predictors allowed us to encompass the physiological limitations of species better. Results: Our models highlighted the additional roles of temperature, primary productivity and dissolved oxygen in shaping fish distributions (average relative contribution to the models of 32.12 ± 10.24, 15.6 ± 7.5 and 12.1 ± 6.1%, respectively). We anticipated a generalized trend of poleward shifts in both future scenarios, with aggravated changes in suitable area with RCP8.5 (average area loss with RCP2.6 = 13.3 ± 4.1%; RCP8.5 = 40.9 ± 13.3%). Shifts to deeper waters were also predicted to be of greater magnitude with RCP8.5 (average depth gain = 25.4 ± 21.5 m) than with RCP2.6 (average depth gain = 10.4 ± 7.9 m). Habitat losses were projected mostly in the Mediterranean, Celtic and Irish Seas, the southern areas of the North Sea and along the NE coast of North America. Main conclusions: Inclusion of biologically meaningful predictors beyond temperature in species distribution modelling can improve predictive performances. Limiting future climate changes by complying with the Paris Agreement can translate into reduced distributional shifts, supporting biodiversity conservation and resource management.
- Biophysical modelling and graph theory identify key connectivity hubs in the Mediterranean marine reserve networkPublication . Abecasis, David; Fragkopoulou, Eliza; Claro, Bruno; Assis, JorgeConnectivity plays a key role in the effectiveness of MPA networks ensuring metapopulation resilience through gene flow and recruitment effect. Yet, despite its recognized importance for proper MPA network functioning, connectivity is not often assessed and is very seldomly used in marine spatial planning. Here, we combined biophysical modelling with graph theory to identify Mediterranean marine reserves that support connectivity between different ecoregions through stepping-stone processes, thus preventing network fragmentation, and those that have an important role as propagule source areas contributing to the recruitment and rescue effects. We identified 19 reserves that play a key role towards the functioning of the network, serving either as stepping-stones or as propagule sources, yet with distinct patterns between ecological groups with contrasting propagule duration (PD). The Cote D'Azur marine reserves are important both as stepping-stones and propagule sources for several ecological groups. Also, key is the Capo Rizzuto and Plemmirio marine reserves due to their role as stepping stones between different marine ecoregions, particularly for species with longer PD (Pisces, Crustacea and Echinodermata). These results provide stakeholders and managers with crucial information for the implementation and management of an efficient marine reserve network in the Mediterranean.
- Carbon density in boreal forests responds non-linearly to temperature: an example from the Greater Khingan Mountains, northeast ChinaPublication . Liu, Yang; Trancoso, Ralph; Ma, Qin; Ciais, Philippe; Gouvêa, Lidiane; Yue, Chaofang; Assis, Jorge; Blanco, Juan A.Boreal forests play a crucial role in the global carbon (C) cycle and in climate stabilization. To better predict global C budgets, it is important to accurately estimate the size of forest C pools, and to identify the factors affecting them. We used national forest inventory data for the Greater Khingan Mountains, northeast China from 1999 to 2018 and 149 additional field plots to estimate C storage and its changes in forest vegetation, excluding C stored in soils, and to calculate the total C density in forest ecosystems. From 1999 to 2018, the vegetation C storage and density increased by 92.22 Tg and 4.30 Mg C ha-1, respectively, while the mean C sink was 4.61 Tg C yr-1. Carbon storage and density showed the same pattern, with the largest stocks in trees, followed by herbs, shrubs, and then litter. Mean C density was higher in mature forests than in young forests. The maximum C density was recorded in Populus davidiana forests, and was 2.2-times larger than in Betula davurica forests (the minimum). The mean (& PLUSMN; standard error) total C density of forest ecosystems was 111.3 & PLUSMN; 2.9 Mg C ha-1, including C stored in soils. Mean annual temperature (MAT) controlled total C density, as MAT had positive effects when it was lower than the temperature of the inflection point (-2.1 to -4.6 degrees C) and negative effects when it was above the inflection point. The rate of change in the total C density depended on the quantile points of the conditional distribution of total C density. Natural and anthropogenic disturbances had weaker effects on C density than temperature and precipitation. In conclusion, our results indicate that there might be a temperatureinduced pervasive decrease in C storage and an increase in tree mortality across Eastern Asian boreal forests with future climate warming.
- Climate-induced range shifts shaped the present and threaten the future genetic variability of a marine brown alga in the Northwest PacificPublication . Song, Xiao-Han; Assis, Jorge; Jie Zhang, Jie; Gao, Xu; Cho, Han-Gil; Duan, De-Lin; Serrao, Ester; Hu, Zi-MinGlaciation-induced environmental changes during the last glacial maximum (LGM) have strongly influenced species' distributions and genetic diversity patterns in the northern high latitudes. However, these effects have seldom been assessed on sessile species in the Northwest Pacific. Herein, we chose the brown alga Sargassum thunbergii to test this hypothesis, by comparing present population genetic variability with inferred geographical range shifts from the LGM to the present, estimated with species distribution modelling (SDM). Projections for contrasting scenarios of future climate change were also developed to anticipate genetic diversity losses at regional scales. Results showed that S. thunbergii harbours strikingly rich genetic diversity and multiple divergent lineages in the centre-northern range of its distribution, in contrast with a poorer genetically distinct lineage in the southern range. SDM hindcasted refugial persistence in the southern range during the LGM as well as post-LGM expansion of 18 degrees of latitude northward. Approximate Bayesian computation (ABC) analysis further suggested that the multiple divergent lineages in the centre-northern range limit stem from post-LGM colonization from the southern survived lineage. This suggests divergence due to demographic bottlenecks during range expansion and massive genetic diversity loss during post-LGM contraction in the south. The projected future range of S. thunbergii highlights the threat to unique gene pools that might be lost under global changes.
- Coastal oceanographic connectivity at the global scale: a dataset of pairwise probabilities and travel times derived from biophysical modelingPublication . Assis, Jorge; Fragkopoulou, Eliza; Serrao, Ester A.; Bastos Araújo, MiguelOcean currents are fundamental drivers of marine biodiversity distribution, mediating the exchange of genetic material and individuals between populations. Their effect ranges from creating barriers that foster isolation to facilitating long-distance dispersal, which is crucial for species expansion and resilience in the face of climate change. Despite the significance of oceanographic connectivity, comprehensive global estimates remain elusive, hindering our understanding of species' dispersal ecology and limiting the development of effective conservation strategies. We present the first dataset of connectivity estimates (including probability of connectivity and travel time) along the world's coastlines. The dataset is derived from Lagrangian simulations of passive dispersal driven by 21 years of ocean current data and can be combined with species' biological traits, including seasonality and duration of planktonic dispersal stages. Alongside, we provide coastalNet, an R package designed to streamline access, analysis, and visualization of connectivity estimates. The dataset provides a new benchmark for research in oceanographic connectivity, enabling a deeper exploration of the complex dynamics of coastal marine ecosystems and informing more effective conservation strategies.
- A concise review of the brown seaweed Sargassum thunbergii — a knowledge base to inform large-scale cultivation effortsPublication . Liu, Fu-Li; Li, Jing-Jing; Liang, Zhou-Rui; Zhang, Quan-Sheng; Zhao, Feng-Juan; Jueterbock, Alexander; Critchley, Alan T.; Morrell, Stephen L.; Assis, Jorge; Tang, Yong-Zheng; Hu, Zi-MinSargassum thunbergii is a brown macroalga endemic to the northwest Pacific. It plays important ecological roles in the structure and maintenance of coastal marine ecosystems. The bioactive compounds extracted from S. thunbergii have been extensively documented for potential use in anti-obesity, anti-inflammatory activity, anti-tumor, anti-oxidant and aquacultural drugs. The species is edible and contains relatively high levels of proteins, minerals and several types of amino acids. The present work compiles recently published literature on S. thunbergii, with particular focus on cultivation efforts in China, including the breeding of seedlings and cultivation at sea. A concise review of possible applications is given. Distribution, range shifts associated with past climate change, population genetic structure and connectivity, life history, reproduction and development are all detailed. The review provides important guidelines for future large-scale farming of S. thunbergii. This will help aquaculturalists (phyconomists) to meet the expected increases in demand by industrial users. It will also help to conserve natural populations which may be declining due to destructive harvesting and rapid ocean changes.
- Corrigendum: Imprint of climate change on Pan-Arctic marine vegetationPublication . Krause-Jensen, Dorte; Archambault, Philippe; Assis, Jorge; Bartsch, Inka; Bischof, Kai; Filbee-Dexter, Karen; Dunton, Kenneth H.; Maximova, Olga; Ragnarsdóttir, Sunna Björk; Sejr, Mikael K.; Simakova, Uliana; Spiridonov, Vassily; Wegeberg, Susse; Winding, Mie H. S.; Duarte, Carlos M.In the original article, there were mistakes in Tables 2–4 and associated legends and text as published. The original article contained errors in the reported modeled macroalgal distribution area in the pan-Arctic and its subregions because the polygons used to calculate the areas were not correctly defined. A correction has been made to Tables 2–4 and their associated legends: The Table legends missed the word “brown” and an explanatory note. The corrected Tables 2–4 and associated legends appear below (corrections marked in bold).
- Cryptic diversity in southern African kelpPublication . Madeira, Pedro; Reddy, Maggie M.; Assis, Jorge; Bolton, John J.; Rothman, Mark D.; Anderson, Robert J.; Kandjengo, Lineekela; Kreiner, Anja; Coleman, Melinda A.; Wernbergh, Tomas; De Clerck, Olivier; Leliaert, Frederik; Bandeira, Salomão; Ada, Abdul M.; Miranda Neiva, João; Pearson, Gareth Anthony; Serrao, Ester A.The southern coast of Africa is one of the few places in the world where water temperatures are predicted to cool in the future. This endemism-rich coastline is home to two sister species of kelps of the genus Ecklonia maxima and Ecklonia radiata, each associated with specific thermal niches, and occuring primarily on opposite sides of the southern tip of Africa. Historical distribution records indicate that E. maxima has recently shifted its distribution similar to 70 km eastward, to sites where only E. radiata was previously reported. The contact of sister species with contrasting thermal affinities and the occurrence of mixed morphologies raised the hypothesis that hybridization might be occurring in this contact zone. Here we describe the genetic structure of the genus Ecklonia along the southern coast of Africa and investigate potential hybridization and cryptic diversity using a combination of nuclear microsatellites and mitochondrial markers. We found that both species have geographically discrete genetic clusters, consistent with expected phylogeographic breaks along this coastline. In addition, depth-isolated populations were found to harbor unique genetic diversity, including a third Ecklonia lineage. Mito-nuclear discordance and high genetic divergence in the contact zones suggest multiple hybridization events between Ecklonia species. Discordance between morphological and molecular identification suggests the potential influence of abiotic factors leading to convergent phenotypes in the contact zones. Our results highlight an example of cryptic diversity and hybridization driven by contact between two closely related keystone species with contrasting thermal affinities.
- A dataset of cold-water coral distribution recordsPublication . Balogh, Viktória; Fragkopoulou, Eliza; Serrao, Ester; Assis, JorgeSpecies distribution data are key for monitoring present and future biodiversity patterns and informing conservation and management strategies. Large biodiversity information facilities often contain spatial and taxonomic errors that reduce the quality of the provided data. Moreover, datasets are frequently shared in varying formats, inhibiting proper integration and interoperability. Here, we provide a qualitycontrolled dataset of the diversity and distribution of coldwater corals, which provide key ecosystem services and are considered vulnerable to human activities and climate change effects. We use the common term cold-water corals to refer to species of the orders Alcyonacea, Antipatharia, Pennatulacea, Scleractinia, Zoantharia of the subphylum Anthozoa, and order Anthoathecata of the class Hydrozoa. Distribution records were collated from multiple sources, standardized using the Darwin Core Standard, dereplicated, taxonomically corrected and flagged for potential vertical and geographic distribution errors based on peer-reviewed published literature and expert consulting. This resulted in 817,559 quality-controlled records of 1,170 accepted species of cold-water corals, openly available under the FAIR principle of Findability, Accessibility, Interoperability and Reusability of data. The dataset represents the most updated baseline for the global cold-water coral diversity, and it can be used by the broad scientific community to provide insights into biodiversity patterns and their drivers, identify regions of high biodiversity and endemicity, and project potential re-distribution under future climate change. It can also be used by managers and stakeholders to guide biodiversity conser-vation and prioritization actions against biodiversity loss. (c) 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )